Difference between revisions of "Team:DUT China B/Model"

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  (2)Except for the initial protein concentration, other factors have the same effect on the binding of the two proteins.</p>
 
  (2)Except for the initial protein concentration, other factors have the same effect on the binding of the two proteins.</p>
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                 <p>The optical control system has the advantages of simple equipment, wireless control, good penetrability, etc., and Chlamydomonas itself has a blue light sensing system, so that the control of the movement of Chlamydomonas cells can be more fully utilized. Since cell micro-nano robots are mainly used in the medical field for targeted therapy, red light is more penetrating than other light tissues and is the most commonly used optical means in the medical field. Therefore, we hope to achieve red color in Chlamydomonas cells. The engineering of light control movement.</p>
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                 <p>Considering the binding of PhyB protein and PIF6 protein in solution, there are/p>
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                 <p>To achieve the kinetic control of Chlamydomonas, how to transform its endogenous motion control and light perception system is the most effective means to achieve our transformation goals. However, because the movement of Chlamydomonas cells is controlled by two flagella, there are three different movement modes of swimming, fluctuation, and sliding under different conditions, and the movement mechanism is complicated. The specific molecular regulation network of two flagella in Chlamydomonas has not been obtained yet. Clear interpretation. Therefore, we cannot start from the molecular mechanism of the Chlamydomonasis movement. In the blue light sensing system of Chlamydomonas, we have learned that the eye spots of Chlamydomonas are used for blue light perception, and then the light signal is transmitted to the flagella to regulate the different movements of the two flagella under the action of the second messenger molecule. Therefore, we try to activate the Chlamydomonas light perception system from the light-gated ion channel at the eye spot to achieve the motion control of Chlamydomonas. But unfortunately, the mutants of the light-gated ion channels have limited redshift range, and we have not been able to find other substances that specifically activate or inhibit the rhodopsin of the Chlamydomonas channel, but only the general purpose of the cells. The second messenger molecule has a regulatory effect on it. We are unable to control the transformation of the universal messenger molecules in the cell, as this can distort the growth regulation of Chlamydomonas cells. So we have to give up on this idea.</P>
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                 <p>If the free concentration of PhyB is A, the free concentration of PIF6 is B, and the concentration of PIF6 is AB, the binding constant is:</P>
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            <p>After encountering a bottleneck in the molecular mechanism transformation, we tried to find a simpler way to control the algae.We have considered that since the channel of rhodopsin is excited by blue light, in the literature search, we have learned the research method of split protein and found the work of splitting luciferase for protein interaction. It is noted that the catalytic reaction of luciferase can produce blue light. We associate it with the possibility of combining red-controlled polymerized proteins with split luciferase. This enables the generation of blue light under red light control. We call this a molecular light converter. By expressing this molecular light converter in Chlamydomonas cells, we can achieve the excitation of endogenous blue light in Chlamydomonas cells, thus realizing the activation and motion control of Chlamydomonas light perception system. Our solution is thus generated.</P>
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                <p>The dissociation constant is</P>
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              <p>Then the expression of the binding rate is</p>
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              <p>Available jointly by (2) (3) (4):</p>
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              <p>Because we assume that the initial concentration of PhyB protein is higher than that of PIF6 protein, that is,</p>
 +
                <p>Available jointly by (5)(6):</p>
 +
              <p>The specific equation between the initial concentration of the two proteins and the binding rate of the two proteins was obtained.Available from (7)</p> 
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              <p>When the light with the wavelength of 650 nm and a frequency of 20 Hz, we know Kd=500nM [1]（fig.1）：</p>
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              <p>The main results are as follows: (1) similar to the barrel effect, the binding rate depends on the low concentration of protein, and it can be estimated from the diagram that the minimum threshold of the concentration of the two proteins is  mol /L at the same time.</p>
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                <p>(2)If the combination rate of A and B is not considered under red light (dark), then </p>
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                <p>Under the excitation of red light,the value is drastically reduced due to the change of in the configuration of the protein ,only when,The combination rate in the dark can be </p>
 +
                  <p>The second part: the combination of N-hrluc and C-hrluc.
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Under the action of "optical switch", the distance between N-hrluc and C-hrluc becomes closer, which is equivalent to increasing the concentration. The effect of "optical switch" on protein binding is explored by using the definition of equivalent concentration to replace the "optical switch".</p>
 
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Revision as of 08:06, 19 October 2019

Document
parts

Introduction

The combination of N-hrluc-PhyB and C-hrluc-PIF3 stimulated by red light can produce blue light and cause microalgae to move.Therefore, the degree of combination of N-hrluc-PhyB and C-hrluc-PIF3 directly determines whether our design is reasonable and the experiment is successful. Based on the simplest chemical thermodynamic formula, the relationship between binding rate and concentration and affinity constant was established in two steps.In addition, as a commonly used photopolymeric protein actuator in photogenetics, our work can not only guide our own experiments, but also provide a simple quantitative model for this field.

Background

The molecular reaction in the solution can be divided into two steps:the first step is red light stimulation of PhyB and PIF3 binding, the second step is that the binding of PhyB and PIF3 facilitates the binding of two parts(NHrluc、Chrluc) of the Sea kidney luciferase. The molecular reactions carried out in our model and solution are also divided into two steps.

The first part: only the binding of PhyB protein and PIF6 protein is considered.

In order to find out the effect of the initial concentration of PhyB protein and PIF3 protein on the binding rate of the two proteins, we considered the binding of only PhyB and PIF3 proteins, and through of two kinds of proteins .Then,we get a specific equation between the initial concentration of protein and the binding rate of the two proteins.

Symbol Meaning
A $ 50,000.00
B $ 10,000.00
Ka $ 85,000.00
Kd $ 56,000.00
A0 $ 98,000.00
B0 $ 98,000.00
PhyB·PIF6 $ 98,000.00
AB $ 98,000.00

Chlamydomonas reinhardtii

(1)After the binding of the two proteins, the solution contains three substances: protein PhyB, protein PIF6 and the combination of the two. That is, the material is conserved and there is no protein loss before and after the reaction.
(2)Except for the initial protein concentration, other factors have the same effect on the binding of the two proteins.

Considering the binding of PhyB protein and PIF6 protein in solution, there are/p>

If the free concentration of PhyB is A, the free concentration of PIF6 is B, and the concentration of PIF6 is AB, the binding constant is:

The dissociation constant is

Then the expression of the binding rate is

Available jointly by (2) (3) (4):

Because we assume that the initial concentration of PhyB protein is higher than that of PIF6 protein, that is,

Available jointly by (5)(6):

The specific equation between the initial concentration of the two proteins and the binding rate of the two proteins was obtained.Available from (7)

When the light with the wavelength of 650 nm and a frequency of 20 Hz, we know Kd=500nM [1]（fig.1）：

The main results are as follows: (1) similar to the barrel effect, the binding rate depends on the low concentration of protein, and it can be estimated from the diagram that the minimum threshold of the concentration of the two proteins is mol /L at the same time.

(2)If the combination rate of A and B is not considered under red light (dark), then

Under the excitation of red light,the value is drastically reduced due to the change of in the configuration of the protein ,only when,The combination rate in the dark can be

The second part: the combination of N-hrluc and C-hrluc. Under the action of "optical switch", the distance between N-hrluc and C-hrluc becomes closer, which is equivalent to increasing the concentration. The effect of "optical switch" on protein binding is explored by using the definition of equivalent concentration to replace the "optical switch".